Spicoli TK

Spicoli TK generates surfaces for molecules and volumes enclosed by these surfaces. Spicoli TK can then apply properties to the surface (hydrogen bonding, polarity/hydrophobicity, charge etc.) Spicoli TK writes out these surfaces attached to the molecule, so the surface and the molecule can be visualized together.

For more detailed information on Spicoli TK, check out the link below:

Documentation

An Example of a result obtained from a combination about modeling toolkits: conformers from Omega TK were overlayed using Shape TK while surfaces and coloring were generated by Spicoli TK.

Modeling

The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore, be used to create new or extend existing functionality associated with those applications.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
OEDocking TK Molecular docking and scoring
Omega TK Conformer generation
Shape TK 3D shape description, optimization, and overlap
SiteHopper TK Rapid comparison of protein binding sites
Spicoli TK Surface generation, manipulation, and interrogation
Spruce TK Protein preparation and modeling
Szybki TK Force field based focused optimization and entropy estimations
OEFF TK Force fields and general optimization tools
Szmap TK Understanding water interactions in a binding site
Zap TK Calculate Poisson-Boltzmann electrostatic potentials
Bioisostere TK 3D fragment similarity, lead optimization, and analog generation
Eon TK Molecular shape and electrostatic overlap

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
OEDepict TK 2D Molecule rendering and depiction
Grapheme™ TK Advanced molecule rendering and report generation
GraphSim TK 2D molecular similarity (e.g. fingerprints)
Lexichem™ TK Name-to-structure, structure-to-name, foreign language translation
MolProp TK Molecular property calculation and filtering
Quacpac TK Tautomer enumeration and charge assignment
OEMedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics
Saiph TK: Extracting, transforming, and loading (ETL) files and records